메뉴 건너뛰기




Volumn 102, Issue 10, 1998, Pages 1797-1805

Rotation of structural water inside a protein: Calculation of the rate and vibrational entropy of activation

Author keywords

[No Author keywords available]

Indexed keywords


EID: 0001455821     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp972948u     Document Type: Article
Times cited : (33)

References (49)
  • 1
    • 0027815738 scopus 로고
    • Hydration of biological macromolecules in solution-surface structure and molecular recognition
    • Wuthrich, K. Hydration of biological macromolecules in solution-surface structure and molecular recognition. Cold Spring Harbor Symp. Quant. Biol. 1993, 58, 149-157.
    • (1993) Cold Spring Harbor Symp. Quant. Biol. , vol.58 , pp. 149-157
    • Wuthrich, K.1
  • 2
    • 0030325741 scopus 로고    scopus 로고
    • Protein hydration dynamics in aqueous solution
    • Denisov, V. P.; Halle, B. Protein hydration dynamics in aqueous solution. Faraday Discuss. 1996, 103, 227-244.
    • (1996) Faraday Discuss. , vol.103 , pp. 227-244
    • Denisov, V.P.1    Halle, B.2
  • 3
    • 0027918556 scopus 로고
    • Water-now you see it, now you don't
    • Levitt, M.; Park, B. H. Water-now you see it, now you don't. Structure 1993, 1, 223-226.
    • (1993) Structure , vol.1 , pp. 223-226
    • Levitt, M.1    Park, B.H.2
  • 4
    • 0024354001 scopus 로고
    • Solvent effects on protein motion and protein effects on solvent motion-dynamics of the active site region of lysozyme
    • Brooks, C. L.; Karplus, M. Solvent effects on protein motion and protein effects on solvent motion-dynamics of the active site region of lysozyme. J. Mol. Biol. 1989, 208, 159-181.
    • (1989) J. Mol. Biol. , vol.208 , pp. 159-181
    • Brooks, C.L.1    Karplus, M.2
  • 5
    • 0027256738 scopus 로고
    • Realistic simulations of native protein dynamics in solution and beyond
    • Daggett, V.; Levitt, M. Realistic simulations of native protein dynamics in solution and beyond. Annu. Rev. Biophys. Biomol. Struct. 1993, 22, 353-380.
    • (1993) Annu. Rev. Biophys. Biomol. Struct. , vol.22 , pp. 353-380
    • Daggett, V.1    Levitt, M.2
  • 6
    • 0027304152 scopus 로고
    • Hydration of proteins-a comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations
    • Brunne, R. M.; Liepinsh, F.; Otting, G.; Wuthrich, K.; vanGunsteren, W. F. Hydration of proteins-a comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. J. Mol. Biol. 1993, 231, 1040-1048.
    • (1993) J. Mol. Biol. , vol.231 , pp. 1040-1048
    • Brunne, R.M.1    Liepinsh, F.2    Otting, G.3    Wuthrich, K.4    VanGunsteren, W.F.5
  • 7
    • 0028921637 scopus 로고
    • Structure and dynamics of the water around myoglobin
    • Phillips, G. N.; Pettitt, B. M. Structure and dynamics of the water around myoglobin. Protein Sci. 1995, 4, 149-158.
    • (1995) Protein Sci. , vol.4 , pp. 149-158
    • Phillips, G.N.1    Pettitt, B.M.2
  • 8
    • 0030057862 scopus 로고    scopus 로고
    • The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation
    • Abseher, R.; Schreiber, H.; Steinhauser, O. The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation. Proteins: Struct., Funct., Genet. 1996, 25, 366-378.
    • (1996) Proteins: Struct., Funct., Genet. , vol.25 , pp. 366-378
    • Abseher, R.1    Schreiber, H.2    Steinhauser, O.3
  • 9
    • 0030604702 scopus 로고    scopus 로고
    • Hydration and DNA recognition by homeodomains
    • Billeter, M.; Guntert, P.; Luginbuhl, P.; Wuthrich, K. Hydration and DNA recognition by homeodomains. Cell 1996, 85, 1057-1065.
    • (1996) Cell , vol.85 , pp. 1057-1065
    • Billeter, M.1    Guntert, P.2    Luginbuhl, P.3    Wuthrich, K.4
  • 10
    • 0030471364 scopus 로고    scopus 로고
    • The role of water in sequence independent ligand binding by an oligopeptide transporter protein
    • Tame, J. R. H.; Sleigh, S. H.; Wilkinson, A. J.; Ladbury, J. E. The role of water in sequence independent ligand binding by an oligopeptide transporter protein. Nat. Struct. Biol. 1996, 3, 998-1001.
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 998-1001
    • Tame, J.R.H.1    Sleigh, S.H.2    Wilkinson, A.J.3    Ladbury, J.E.4
  • 11
    • 0026326956 scopus 로고
    • Protein hydration in aqueous solution
    • Otting, G.; Liepinsh, E.; Wuthrich, K. Protein hydration in aqueous solution. Science 1991, 254, 974-980.
    • (1991) Science , vol.254 , pp. 974-980
    • Otting, G.1    Liepinsh, E.2    Wuthrich, K.3
  • 12
    • 0028921999 scopus 로고
    • Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR
    • Ernst, J. A.; Clubb, R. T.; Zhou, H. X.; Gronenborn, A. M.; Clore, G. M. Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR. Science 1995, 267, 1813-1817.
    • (1995) Science , vol.267 , pp. 1813-1817
    • Ernst, J.A.1    Clubb, R.T.2    Zhou, H.X.3    Gronenborn, A.M.4    Clore, G.M.5
  • 13
    • 0029994817 scopus 로고    scopus 로고
    • Using buried water molecules to explore the energy landscape of proteins
    • Denisov, V. P.; Peters, J. Horlein, H. D.; Halle, B. Using buried water molecules to explore the energy landscape of proteins. Nat. Struct. Biol. 1996, 3, 505-509.
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 505-509
    • Denisov, V.P.1    Peters, J.2    Horlein, H.D.3    Halle, B.4
  • 14
    • 0029081424 scopus 로고
    • Residence times of the buried water molecules in bovine pancreatic trypsin inhibitor and its G36S mutant
    • Denisov, V. P.; Halle, B. Residence times of the buried water molecules in bovine pancreatic trypsin inhibitor and its G36S mutant. Biochemistry 1995, 34, 9046-9051.
    • (1995) Biochemistry , vol.34 , pp. 9046-9051
    • Denisov, V.P.1    Halle, B.2
  • 15
    • 0028948786 scopus 로고
    • Protein hydration dynamics in aqueous solution-a comparison of bovine pancreatic trypsin inhibitor and ubiquitin by O-17 spin relaxation
    • Denisov, V. P.; Halle, B. Protein hydration dynamics in aqueous solution-a comparison of bovine pancreatic trypsin inhibitor and ubiquitin by O-17 spin relaxation. J. Mol. Biol. 1995, 245, 682-697.
    • (1995) J. Mol. Biol. , vol.245 , pp. 682-697
    • Denisov, V.P.1    Halle, B.2
  • 16
    • 0028937274 scopus 로고
    • Hydrogen exchange and protein hydration-the deuterium spin relaxation dispersions of bovine pancreatic trypsin inhibitor and ubiquitin
    • Denisov, V. P.; Halle, B. Hydrogen exchange and protein hydration-the deuterium spin relaxation dispersions of bovine pancreatic trypsin inhibitor and ubiquitin. J. Mol. Biol. 1995, 245, 698-709.
    • (1995) J. Mol. Biol. , vol.245 , pp. 698-709
    • Denisov, V.P.1    Halle, B.2
  • 17
    • 0021603710 scopus 로고
    • Structure of Bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II
    • Wlodaver, A.; Walter, J. Huber, R.; Sjolin, L. Structure of Bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II. J. Mol. Biol. 1984, 180, 301-329.
    • (1984) J. Mol. Biol. , vol.180 , pp. 301-329
    • Wlodaver, A.1    Walter, J.2    Huber, R.3    Sjolin, L.4
  • 18
    • 0000231955 scopus 로고
    • Conjugate Peak Refinement-an algorithm for finding reaction paths and accurate transition-states in systems with many degrees of freedom
    • Fischer, S.; Karplus, M. Conjugate Peak Refinement-an algorithm for finding reaction paths and accurate transition-states in systems with many degrees of freedom. Chem. Phys. Lett. 1992, 194, 252-261.
    • (1992) Chem. Phys. Lett. , vol.194 , pp. 252-261
    • Fischer, S.1    Karplus, M.2
  • 19
    • 5544255138 scopus 로고
    • The structure of ice Ih by neutron diffraction
    • Kuhs, W. F.; Lehmann, M. S. The structure of ice Ih by neutron diffraction. J. Phys. Chem. 1983, 87, 4312-4313.
    • (1983) J. Phys. Chem. , vol.87 , pp. 4312-4313
    • Kuhs, W.F.1    Lehmann, M.S.2
  • 20
    • 33845280068 scopus 로고
    • Observation of molecular reorientation in ice by proton and deuterium magnetic resonance
    • Wittebort, R. J.; Usha, M. G.; Ruben, D. J.; Wemmer, D. E.; Pines, A. Observation of molecular reorientation in ice by proton and deuterium magnetic resonance. J. Am. Chem. Soc. 1988, 110, 5668-5671.
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 5668-5671
    • Wittebort, R.J.1    Usha, M.G.2    Ruben, D.J.3    Wemmer, D.E.4    Pines, A.5
  • 21
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • Brooks, B. R.; Janezic, D.; Karplus, M. Harmonic analysis of large systems. I. Methodology. J. Comput. Chem. 1995, 16, 1522-1542.
    • (1995) J. Comput. Chem. , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janezic, D.2    Karplus, M.3
  • 24
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free energies in molecular systems
    • Neria, E.; Fischer, S.; Karplus, M. Simulation of activation free energies in molecular systems. J. Chem. Phys. 1996, 105, 1902-1921.
    • (1996) J. Chem. Phys. , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 26
    • 0011776553 scopus 로고
    • Reorientation of water molecules in solid hydrates-correlation with spectroscopic and structural data
    • Larsson, K.; Tegenfeldt, J.; Hermansson, K. Reorientation of water molecules in solid hydrates-correlation with spectroscopic and structural data. J. Chem. Soc., Faraday Trans. 1991, 87, 1193-1200.
    • (1991) J. Chem. Soc., Faraday Trans. , vol.87 , pp. 1193-1200
    • Larsson, K.1    Tegenfeldt, J.2    Hermansson, K.3
  • 27
    • 84988057883 scopus 로고
    • Spatially constrained minimization of macromolecules
    • Bruccoleri, R. E.; Karplus, M. Spatially constrained minimization of macromolecules. J. Comput. Chem. 1986, 7, 165-175.
    • (1986) J. Comput. Chem. , vol.7 , pp. 165-175
    • Bruccoleri, R.E.1    Karplus, M.2
  • 28
    • 0000715079 scopus 로고    scopus 로고
    • Calculation of the reaction pathway for the aromatic ring flip in methotrexate complexed to dihydrofolate reductase
    • Verma, C. S.; Fischer, S.; Caves, L. S. D.; Roberts, G. C. K.; Hubbard, R. E. Calculation of the reaction pathway for the aromatic ring flip in methotrexate complexed to dihydrofolate reductase. J. Phys. Chem. 1996, 100, 2510-2518.
    • (1996) J. Phys. Chem. , vol.100 , pp. 2510-2518
    • Verma, C.S.1    Fischer, S.2    Caves, L.S.D.3    Roberts, G.C.K.4    Hubbard, R.E.5
  • 29
    • 0028670805 scopus 로고
    • Cis-trans imide isomerization of the proline dipeptide
    • Fischer, S.; Dunbrack, R.; Karplus, M. Cis-trans imide isomerization of the proline dipeptide. J. Am. Chem. Soc. 1994, 116, 11931-11937.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 11931-11937
    • Fischer, S.1    Dunbrack, R.2    Karplus, M.3
  • 30
    • 0013517679 scopus 로고
    • Reaction path study of helix formation in tetrapeptides-effect of side chains
    • Choi, C.; Elber, R. Reaction path study of helix formation in tetrapeptides-effect of side chains. J. Chem. Phys. 1991, 94, 751-760.
    • (1991) J. Chem. Phys. , vol.94 , pp. 751-760
    • Choi, C.1    Elber, R.2
  • 31
    • 11744336984 scopus 로고    scopus 로고
    • Manuscript in preparation
    • Fischer, S. Manuscript in preparation.
    • Fischer, S.1
  • 35
    • 0842265496 scopus 로고
    • Classical and modern methods in reaction rate theory
    • Berne, B. J.; Borkovec, J. E.; Straub, J. E. Classical and modern methods in reaction rate theory. J. Phys. Chem. 1988, 92, 3711-3725.
    • (1988) J. Phys. Chem. , vol.92 , pp. 3711-3725
    • Berne, B.J.1    Borkovec, J.E.2    Straub, J.E.3
  • 36
    • 0001691292 scopus 로고    scopus 로고
    • Unit cells for simulation of hexagonal ice
    • Hayward, J. A.; Reimers, J. R. Unit cells for simulation of hexagonal ice. J. Chem. Phys. 1997, 106, 1518-1529.
    • (1997) J. Chem. Phys. , vol.106 , pp. 1518-1529
    • Hayward, J.A.1    Reimers, J.R.2
  • 37
    • 0028360307 scopus 로고
    • The contribution of vibrational entropy to molecular association: The dimerization of insulin
    • Tidor, B.; Karplus, M. The contribution of vibrational entropy to molecular association: the dimerization of insulin. J. Mol. Biol. 1994, 238, 405-414.
    • (1994) J. Mol. Biol. , vol.238 , pp. 405-414
    • Tidor, B.1    Karplus, M.2
  • 39
    • 0030442990 scopus 로고    scopus 로고
    • Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures
    • Hooft, R. W. W.; Sander, C.; Vriend, G. Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins: Struct., Funct., Genet. 1996, 26, 363-376.
    • (1996) Proteins: Struct., Funct., Genet. , vol.26 , pp. 363-376
    • Hooft, R.W.W.1    Sander, C.2    Vriend, G.3
  • 40
    • 0009502708 scopus 로고
    • Effects of defects on molecular mobility in liquid water
    • Sciortino, F.; Geiger, A.; Stanley, H. E. Effects of defects on molecular mobility in liquid water. Nature 1991, 354, 218-221.
    • (1991) Nature , vol.354 , pp. 218-221
    • Sciortino, F.1    Geiger, A.2    Stanley, H.E.3
  • 41
    • 33748555581 scopus 로고    scopus 로고
    • Tetrahedral displacement-the molecular mechanism behind the debye relaxation in water
    • Agmon, N. Tetrahedral displacement-the molecular mechanism behind the debye relaxation in water. J. Phys. Chem. 1996, 100, 1072-1080.
    • (1996) J. Phys. Chem. , vol.100 , pp. 1072-1080
    • Agmon, N.1
  • 42
    • 0028986918 scopus 로고
    • Internal mobility of the basic pancreatic trypsin inhibitor in solution-a comparison of NMR spin relaxation measurements and molecular dynamics simulations
    • Smith, P. E.; vanSchaik, R. C.; Szyperski, T.; Wuthrich, K.; vanGunsteren, W. F. Internal mobility of the basic pancreatic trypsin inhibitor in solution-a comparison of NMR spin relaxation measurements and molecular dynamics simulations. J. Mol. Biol. 1995, 246, 356-365.
    • (1995) J. Mol. Biol. , vol.246 , pp. 356-365
    • Smith, P.E.1    Vanschaik, R.C.2    Szyperski, T.3    Wuthrich, K.4    Vangunsteren, W.F.5
  • 43
    • 0000127140 scopus 로고
    • Method for estimating the configurational entropy of macromolecules
    • Karplus, M.; Kushik, J. N. Method for estimating the configurational entropy of macromolecules. Macromolecules 1981, 14, 325-332.
    • (1981) Macromolecules , vol.14 , pp. 325-332
    • Karplus, M.1    Kushik, J.N.2
  • 44
    • 33748374124 scopus 로고
    • Statistical mechanics of isomerization dynamics in liquids and the transition state approximation
    • Chandler, D. Statistical mechanics of isomerization dynamics in liquids and the transition state approximation. J. Chem. Phys. 1978, 68, 2959.
    • (1978) J. Chem. Phys. , vol.68 , pp. 2959
    • Chandler, D.1
  • 45
    • 11744249583 scopus 로고
    • Ph.D. Thesis, Harvard University, Cambridge, MA
    • Fischer, S. Ph.D. Thesis, Harvard University, Cambridge, MA, 1992.
    • (1992)
    • Fischer, S.1
  • 46
    • 0027742843 scopus 로고
    • A Mechanism for rotamase catalysis by the FK506 binding protein (FKBP)
    • Fischer, S.; Michnick, S.; Karplus, M. A Mechanism for rotamase catalysis by the FK506 binding protein (FKBP). Biochemistry 1993, 32, 13830-13837.
    • (1993) Biochemistry , vol.32 , pp. 13830-13837
    • Fischer, S.1    Michnick, S.2    Karplus, M.3
  • 49
    • 0031556719 scopus 로고    scopus 로고
    • Orientational disorder and entropy of water in protein cavities
    • Denisov, V. P.; Venu, K.; Peters, J.; Horlein, H. D.; Halle, B. Orientational disorder and entropy of water in protein cavities. J. Phys. Chem. B 1997, 101, 9380-9389.
    • (1997) J. Phys. Chem. B , vol.101 , pp. 9380-9389
    • Denisov, V.P.1    Venu, K.2    Peters, J.3    Horlein, H.D.4    Halle, B.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.